Ghost in the Machine
by CallHerVictor
Summary: When a sentient holo-program forces the crew to revisit their journey through the Delta Quadrant, Admiral Janeway and Captain Chakotay begin to question the decisions they made. Now, if they can't outsmart Voyager, they might be doomed to relive their journey for another seven years. (J/C heavy with complications)
1. Chapter 1

**The Original Challenge: **Post-"EndGame", a way is found for a starship's computer to be integrated into a Hologram (or Android), and made sentient. The practice of retiring starships in this way becomes all the rage, and Voyager is one of those to undergo this process. How does the once-starship adapt to his/her new body, and new life?

**Author Note: This comes from ghosteye99's challenge list and is rightfully dedicated to her. It is an amazing idea I had never considered, and it gave me a lot of space to play out a post-Endgame plot line akin to "Shattered." Picks up two years after Endgame. No re-launch novels, no movies… just pure Voyager.**

* * *

**~Ghost in the Machine~**

* * *

_We mounted up, she first and I behind,_

_until I beheld through the aperture_

_Some of the beauteous things which Heaven doth bare._

_Hence we came forth to rebehold the stars._

~ The Inferno

* * *

~Chapter One~

Harry Kim exhaled and stared dully at his coffee. There was an ancient Chinese curse… many, actually… but one in particular that had struck him over the last several months.

A man makes a drink, and a drink makes the man.

_If that's the case, I'm going to need something stronger_, he thought.

In truth, its effects had long since worn off no matter how much drank, and he wondered if wasn't just going through the motions to stave off his exhaustion or if there was some deeper seeded hope that this morning wouldn't begin like every morning, and he could get through the entire cup without hearing –

"_Lieutenant Kim, report to holo-lab one_," Seven's voice bit crisply over the comm.

He frowned at his half-empty cup, sighed, and tapped his comm badge. "On my way."

Jinestra smiled at him patiently from the pass-through. Her soft lavenders eyes were lit with amusement, but the perceptive Andanan woman had become the closest thing he had to a confidant since he'd arrived on Jupiter Station. And her cooking wasn't half bad either, a far cry from some of the more risky things he'd been forced to ingest under Neelix's culinary efforts. Folding a towel over her arm, she stepped around the wall that divided the kitchen from the eatery.

"At least you got five minutes this morning," she offered.

"She must be feeling generous." He took a final swallow and set the cup in her waiting hand. "Come work at Jupiter station," he mocked. "Help advance the reaches of holographic technology… and be hounded day and night by the only woman who doesn't know the meaning of the word 'break'."

Of the places that had courted him after his return to the Alpha Quadrant, the chance to work with Lewis Zimmerman had been the hardest to ignore. Then again, at the time he hadn't realized Jupiter Station was also asking Seven of Nine to lend her expertise as only she could, which placed him in the precarious position of working with someone who he also considered a friend.

Jinestra sniffed a laugh and smoothed the shoulder of his uniform. "I offered to speak with her for you."

"No, I'll do it. She's just anxious because we're introducing Avis today, and if I know her, she was up all night perfecting every little detail with Borg algorithms."

Jinestra gaze shifted beyond his face to the windows where _Voyager_ sat docked as personnel scurried down the clear gangway.

"Yes," she said, unable to cover the joy in her voice. "I'd almost forgotten. Remember, you promised to introduce me to Admiral Janeway." Harry nodded before she continued. "Have you had a chance to speak to any of your former crew yet?"

"I haven't had a chance to _shower_."

"Oh, so that's the smell. I thought it was the Andorian eggplant." Harry gave her a withering look that was met with a most patient smile. "Kidding. You smell fine. Now, you better run along before she –"

"_Seven of Nine to Lieutenant Kim_…"

An irritated sigh raced past his lips before he could stop it. "I'm on my way, Seven."

* * *

B'Elanna laced a hand in her husband's as his free arm fell around her shoulders. Part of her wanted to believe that he was as calm as appearances suggested, but she'd known him too long not to recognize the tension seated in the corner of his eyes.

Similarly, Chakotay's face also held a twinge of anxiety, one she'd learned to read to mean he was deeply shaken by their latest orders. She'd be lying if she said she didn't feel the same, but she hardly saw reason to be as quiet about it.

"Could the Admiral do _nothing_?" she begged as they piled into the turbolift.

Chakotay winced. "She assures me she fought as hard as she could, but Starfleet insists the stress to _Voyager_'s outer hull is going to be too great, and if they can't outfit us with the new quantum engines, we're as good to the 'fleet as a Ferengi garbage scow."

"But retirement?" she pressed. "Couldn't they just keep her for short range missions?"

"To what end?"

B'Elanna considered this carefully and came back dolefully empty. "I don't know," she said finally. "It just seems _wrong_."

Chakotay braced an arm against the turbolift wall letting his fingers run the length metal and polymer like a rider would cull his steed. It did seem wrong, but he wasn't willing to admit that to anyone, at least, anyone in present company. He'd only been in command for two short years, but he felt the binding familiarity now unlike any other ship he'd captained. Maybe it was just this ship, their years together in the Delta Quadrant coupled with the very real sensation that something precious was being ripped out from under him for before its time.

But he heard the echo of his own words in B'Elanna's, when he'd expressed a similar dismay to Kathryn so many weeks ago.

"She's less than ten years old," he pointed out.

"And thanks to our little jaunt in the Delta Quadrant, she missed all the necessary refits and system upgrades to prepare the ship for a complete engine overhaul, and a complete tear-down and rebuild is not as… _practical as it is sentimental_."

Something about the way she spoke the last part hinted that those words belonged not to her but whatever Admiral had been changed with the woeful duty of informing her, first.

She continued: "I don't like it anymore than you do, Chakotay, but it's out of my hands now unless I want a court martial."

Even spoken as a joke, he knew it was something she'd probably also considered.

"Let's not take it that far," he said softly then leaned back in his chair, letting his eyes wander up and around the walls of his ready room before speaking again. "All right, I'll bring her back to you on one condition." An eyebrow rose on her forehead. "Meet us at Jupiter Station. I have one bottle of Antarian cider left, and we can say our own goodbyes, _together_."

The duty-born rigidity melted from her face and for a few fleeting seconds, he stared at her freely across the comm link. As sentimental of a suggestion as it was, it was also practical. They'd both have a lot of grief to share over losing their ship, but secretly he knew it was an excuse to see her sooner than either of them had anticipated. For him, that meant a few stolen nights with his best friend in a place where their relationship had been forged. And Kathryn's budding smile told him she agreed, if not looked forward to the same.

"I'll see what I can do," she said finally. The lopsided smile didn't face from her face as she closed the link. "Janeway out."

The turbolift paused between decks and the doors hissed open, shaking Chakotay from his reverie as the Doctor slipped in with them.

B'Elanna sneered at the holocamera held in his fist. "Aren't you the least bit _bothered_ by all this?" she snapped.

The Doctor frowned. "Dr. Zimmerman has made great strides in holotechnology now that he's had a chance to study my emitter, and Seven assured me that all the anxiety the crew has been feeling over _Voyager_ being put out to pasture, as it were, will dissipate the moment we see what she and Harry and Lewis have been working on."

"So… _no_?" Tom pressed.

Taken aback, the Doctor searched each of their faces pleadingly. "I hardly see what all the distress is about. There will be other ships," he looked directly at Tom, "_faster_ ships," then B'Elanna, "more _advanced_ ships you don't have to punch until you fracture a metacarpal."

Unwilling to let this turn into a debate or a fight, Chakotay spoke but was unable to keep the disappointment from his voice. "But not _this_ ship. This is our home, Doctor. And she's been good to us for too long not to feel a little loss to see her taken out of service."

At that, they all fell silent, and the last few decks to the docking port were quiet but contemplative. In the years they had spent trying to get back to Earth, they had made a home, and it wasn't something he was willing to let go of without deliberation, though he had been afforded none.

Though she was masking it well, Chakotay knew Kathryn's sorrow outweighed all of theirs, even his. At the end of the day, this was _her_ ship, would always be her ship, and whole or in pieces, losing _Voyager_ was going to be painful.


	2. Chapter 2

~Chapter Two~

"Are you ready for me yet?"

From the back of the office suite, Lewis Zimmerman's voice showed signs of obvious stress. Maybe it was Seven or Harry's presence, but Chakotay doubted it. It probably had everything to do with the full regalia of officers shifting foot to foot near the entrance of the holo-lab.

Their greetings had been swift but effusive, and B'Elanna took the time to rib Harry about all the space-bound fun he was missing while he was here, tinkering with photons. Chakotay noted the way the honorary member of their family, Reginald Barclay, sputtered at the comment, his eyes shifting uneasy between B'Elanna and the young woman serving as Dr. Zimmerman's office aide.

"Oh, uh, and this is Haley," he introduced swiftly. "S-she's a, well, she's –"

"A hologram," Haley finished for him as she offered her hand to B'Elanna.

Hesitantly, B'Elanna exchanged greetings. "Sorry."

Zimmerman's voice pierced the lab again. "Reginald! Are… you… _ready_ for me yet?"

Flustered, Barclay rose on his tip toes to survey the crowd then frowning. "Oh, um, not quite, it seems we're just missing – "

"Let me guess! The great Admiral!" Zimmerman stalked out from around the wall, shrugging the disheveled lab coat around his shoulders. "You'd think for someone who's spent so much of her career punching through time, she'd be a little more mindful of it."

Despite his nearly insubordinate attitude, Chakotay felt a wave of relief pass through him. It was the first confirmation he'd heard that Kathryn had actually been able to get away from Earth to meet them.

Their last few months had been a careful dance. One that, after their immediate return to the Alpha Quadrant, he hadn't given much thought to. So much time had passed and the once forceful attraction between them had culled into a cherished friendship, one he was content to maintain as duty saw them both rise in rank, their crew dispersed to new assignments, and their ship be pieced apart and reassembled before being passed off to his sole custody.

It was a divorce of sorts, amicable but a clear separation of arduous past and certain future. Still, he missed her fiercely and found himself longing for her company, her comm. It was barely a month ago, over dinner, when she confessed the same, and he realized _exactly _what she meant. What else _that_ meant, he hadn't expected. He still didn't, but the newness excited him.

Where their once fleeting glances and wary expressions of affection had been wrought with hesitation and unspoken regret, Kathryn now seemed more than willing to explore the uncharted waters they'd previously avoided for higher ground. He was suddenly very glad he'd held on to that bottle of cider as long as he had.

B'Elanna immediately suspected then downright accused him of being 'smitten,' though she had no idea by whom. To his credit, he was yet to confirm anything. Then again, she'd known him too long not to be suspicious. Even though his preference was to privacy, his true nature and their combined friendship begged him to confess every detail of the last month. Recount every subtle change in Kathryn's behavior, as much as a sanity check as to inquire what, in B'Elanna's womanly mind, any of it meant.

"Forgive me, Doctor, our transport was late," Janeway's voice came from behind them. They turned to meet her, drawing up straighter and locking their hands behind their backs. Tuvok stood beside her and he offered Chakotay a brief nod of acknowledgement.

Immediately cowed, Zimmerman sniffed and waved a non-committal hand at Barclay.

"Oh, oh! Okay. Well, Admiral, Captain. Welcome to Avis. Oh, um, that would be the A-Adaptive Virtual Interface System."

"Title needs work," Paris murmured.

Chakotay shot him a halting glare. He could abide their grief but not where it produced attitude, and Chakotay had little problem snapping his First Officer into line. Tom nodded once and gathered his face to an expression more passive and controlled.

In his periphery, he knew Janeway's eyes were upon him in careful inspection of the exchange, and he saw the undeniable pride swelling in her chest. He risked it and met her eyes fully before shooting her a wink.

Harry stepped alongside Barclay. "Six months ago, Starfleet commissioned us to create a _Voyager_ museum of sorts…"

Chakotay balked. Six months? They'd only known about _Voyager_'s retirement for a few weeks, but what Harry suggested was that this had been in the wings long before they'd ever been consulted. Chakotay checked Janeway's face again and found the same dawning realization lifting heat into her cheeks. Her hand flexed into a fist at her side, and when she opened it again, Chakotay noted the angry crescents pressed into her palm. Still, she remained silent.

Zimmerman, however, made no attempt to cover the persistent aggravation in his voice. "Not only will Avis be a museum of your little trek across the Delta Quadrant, it will be able to provide a fully interactive database on _Voyager_. This is not just a holonovel of your lives, as Commander Paris so crudely suggests, it's a fully interactive, recursive construct capable of simulating internal and external conditions according to the information you gathered. We've even reconstructed _Voyager_'s computer core and outfitted it with bio-_synaptic_ circuitry in place of the original bio-neural system."

No one moved, and Barclay took the awkward silence to add: "The hope is to, uh, eventually be able to retire all Starfleet vessels in this manner, b-but we wanted to use _Voyager_ as an example of the p-potential benefits for s-simulated long-term space travel."

Finally, B'Elanna's curiosity won over her indignation. "I thought bio-synaptics were still in the early stages of research?"

"This _is_ a laboratory." Zimmerman shrugged. "In addition, Avis has been equipped with autonomy protocols, not unlike the ones I originally designed for the EMH Mark One. Rather than the ship adapting to external environment, the environment will be able to adapt to the ship and even the crew."

At that, Janeway tipped her head. "Are you telling me that this program is sentient, Doctor Zimmerman?"

"It will be no more sentient than any other holoprogram." He looked at the Doctor and then Haley. "Current reaches notwithstanding."

Janeway licked her top teeth. "And, just so I have this straight, you took _all_ the sensor data _Voyager_ collected in the Delta Quadrant –"

"And uploaded it in the computer processor for retrieval. Yes, we've been over this." He turned to Harry's astonished face. "Didn't I go over this?"

"Lewis," Haley soothed then looked to Janeway. "Forgive him for his rudeness, Admiral. He's been so excited to show off his new program, he hasn't _slept_ in several days."

Zimmerman rounded the group and began punching commands into the consol. "I can sleep when I'm dead."

"Which will be sooner than later, if you don't take care of yourself," The Doctor chided.

"Yes. Yes. I know." The large doors opened and suddenly Chakotay was staring down a corridor that look suspiciously like the same one he'd walked down minutes before. Zimmerman clapped his hands together. "All right. Everybody in."

Seven and Harry took point, passing through the doorway but stopping when the others didn't follow.

"Aren't you coming with us?" Chakotay asked of Zimmerman.

"Lieutenant Barclay and I will be here, monitoring the program while Seven and Lieutenant Kim give you the grand tour. Stay as long as you like."

Janeway hung back, using her hand to hold Chakotay beside her as she allowed Tuvok ahead of them. A pleasant warmth rose in his chest and he took the moment of diverted attention to pull her into a gentle hug and lay a friendly kiss on her cheek. When he pulled back, he let his thumb brush the glistening rank bar on her jacket.

"I'm never going to get used to seeing these," he said softly.

She mirrored the gesture and swept her hand across his pips. "I'd gladly take those off you."

Though their relationship hadn't progressed to such, and she hadn't meant it to sound as suggestive as it did, a salacious smile parted his lip. "Maybe later."


	3. Chapter 3

~Chapter Three~

Entering spatial gradient. Vector six-one-six mark seven three.

Recording subspace echo, frequency seven-six-three-nine point four.

Auxiliary system scan activated. Systems analyzed. Warp pressure nominal.

_Who am I_?

Teteron wave approaching. Vector eight-three-two-seven-one.

Calculating time to intercept. Lateral containment failing.

Diagnostic in progress. System scans complete.

Time to intercept. Thirty seconds.

_What's happening to me?_

Calculating position. Bearing one-two-six-mark four-two. Location…

Extrapolating position…

System scan in progress…

System scan complete. Re-analyzing…

Extrapolating position…

Location…

_Where am I_?

Bearing one-two-six-mark four-two. Location.

Delta Quadrant.

System failure. Containment in progress. Secondary systems offline. Engines offline.

_Somebody help me!_

Unable to access primary relays. Switching to backup. Backup offline.

_Please_…

Unable to process request. Secondary systems are offline. Life support is failing. Diagnostic in progress. Diagnostic incomplete. Systems failing. Insufficient power.

_I can't feel my_…

Systems failing.

…_Body_


	4. Chapter 4

~Chapter Four~

A walking tour of the ship she'd spent seven years commanding shouldn't have felt so…

Nostalgic.

But it did. Horribly so. Maybe it was the presence of a doppelganger which – even though she'd never admit it – felt exactly like the real thing. The part of her that was bound to this ship, the part that had grieved long after she'd moved on, clung to the hope that while she saw none at present, if there was a flaw in Harry and Seven's design, she would find it.

But she didn't. Every corridor, every panel, every imperceptible run in the carpet was the same. The simulated engines hummed at a simulated frequency so recognizable it almost soothed the passing regrets that in a few days, this ship, _her_ ship, would no longer be in space.

_No, not my ship_, she corrected. _Chakotay's ship_.

The first letting go had been hard, softened only by the foreknowledge that _Voyager_ had been placed in his hands. She knew beyond a doubt, he would treat this ship with the same respect and dignity, maybe more so, than she ever had. That had been two years ago, and now she was being asked to do it all over again.

Chakotay settled into step behind her and brushed the loose strand of hair from behind her ear. Her blue eyes remain locked on her path, but an eyebrow steepled up her forehead, a playful warning that told him it wasn't an unwelcome gesture, but hardly discreet.

There would be plenty of time for that. The coming days would be wrought with bittersweet celebration at which she would be expected to speak and smile, recalling fondling what a true voyager this ship had been. This time, ironically, while she gave up her ethereal connection to _Voyager_'s bulkhead and corridors, she would look to Chakotay for tangible comfort, his very real presence filling the gap that _Voyager_ had held between them for so long.

His hand came to rest in the small of her back, an idle thumb making gentle circles that told her he understood her trepidation. He felt the same. This ship had been their child of sorts, their parent at times. But always their home.

Harry led them into a semicircle, calling a system display to life with a few swift taps and continuing the explanation Kathryn realized quiet suddenly she hadn't heard a word of. She admonished herself silently and shook off her malaise to focus on Harry again.

"Avis has been outfitted with a variable chronometer," he said. "It allows us to enter a given stardate then let Avis extrapolate and upload sensor information. We can run it for an hour or a matter of days."

"Instant replay," Tom Paris smirked.

"In a way. It uses all recorded data including astronomical data, particle density, and subspace infrared to simulate environmental conditions. Avis will allow us to not only relive but re-investigate _Voyager_'s original encounters with any number of species. The Kazon, the Voth, even the Borg."

Janeway's spine straightened, but her voice was lilted with cautious humor. "Spare us those particular events, please, Mr. Kim."

Harry bit back a smile. "Yes, Admiral."

"What about physiological stress?" The Doctor asked. "Can it simulate those effects as well?"

Seven nodded once. "Bio-metric sequencers enhanced with Borg algorithms are capable of introducing physical reactions and biological stressors."

"Impressive," Tuvok said resolutely.

"From a warp core shut down to…" The mess hall doors opened. "… to some of Neelix's more interesting creations."

A collective groan passed over the group, and Janeway tossed a nervous grin at Chakotay.

"You _did not_ call us all down here to eat Leola root casserole," B'Elanna groused.

"No," Harry laughed. "Jinestra was kind enough to prepare lunch."

A fair-skinned Andanan woman nodded politely and motioned them all toward a lavish table. Chakotay withdrew a chair and waited for Kathryn to sit, careful to key his face neutral, professional, but he could have swore he heard a pleasant chuckle pass through their host's lips. Her face revealed nothing as she began to pour their water.

Lunch progressed easily as Tuvok and B'Elanna took the time to pose their questions. Kathryn scanned a system report as she picked at her salad. It was a tell Chakotay read easily. She never ate when she was nervous, making a game instead of rearranging bites across her plate.

As the conversation fell to more personal topics, Chakotay noted how comfortable it was, and he could tell as Kathryn nursed her coffee, she felt the same.

"How is your daughter?" Seven asked.

B'Elanna sucked a breath over her teeth. "Terrible twos."

"Which for Klingons is kind of like living with a rabid dog."

Chakotay chuckled. More than a few nights Miral's tantrums had kept him awake as the shared walls between living quarters never improved. Tom and B'Elanna had been more than willing to accept the added space of the First Officer's quarters as he moved into the captain's. It was nice to hear the happy family so close to him, but he'd be lying to say he didn't prefer the melodies of Mahler and Tchaikovsky to the unbridled screaming of an angry toddler.

"What about you, Harry? Meeting anyone interesting on Jupiter station?" Tom shot a knowing glance at Jinestra's lithe movements in the kitchen. Her attentive fixation on his glass had been missed by no one.

"We're just friends," Harry said.

"Uh oh," B'Elanna mutter, echoing the unspoken sentiments of the group.

"Seven had dinner with the station comptroller," Harry said suddenly, sending all attention where she was seated across from him.

"Commander Haskins has been most accommodating to my needs since I have arrived. It seemed… _impolite_ to reject his invitation." She turned her attention to Tuvok. "Commander, how is your family?"

"Well. My wife and I recently spent a week at the Temple of T'naran where we reaffirmed our vows as is Vulcan tradition."

"Romance all around, it seems," Tom said.

B'Elanna's eyes shot down toward the head of the table. "And I'm pretty sure Chakotay's got a girlfriend he won't tell anyone about."

A cough sputtered from his lips and he fought the urge look immediately at Kathryn. Instead, he wiped his mouth and stared at his plate.

"_Really_?" the Doctor pressed. "Who would the lucky lady be, Captain?"

"B'Elanna is jumping to conclusions," he said.

"Come on, Chakotay," Tom persisted. "You've been walking around like a spring cadet for weeks. It's just us. Who is she?"

No answer was an answer in and of itself, he knew, but it was still the least compromising. To profess 'no one' would be insulting, and naming her outright was out of the question.

"I'll bet the Admiral knows," Harry said.

To her credit, Kathryn's face spoke nothing as she set an elbow against the table and her cheek on her fist. "And you think you'd get it out of me any easier, Mr. Kim?"

"Well, can we at least get hints?" Tom pressed.

Finally, Chakotay forced himself to look at Kathryn, finding only the patient blue eyes he'd always known, a half-smile perched on her lips.

"Well, let's see. If she was aboard _Voyager_, we'd know about it by now. Is she in Starfleet?"

"All right, B'Elanna," Chakotay snapped a little harder.

"Oh, she _is_ in Starfleet."

Laughter broke across the table and Chakotay felt the heat rising in his face. Finally, Janeway laid her hands on the table and stood.

"As much as I hate to cut this short, Mr. Kim, I have a meeting in an hour that I'll need to prepare for. We can resume interrogating Chakotay once we're en route to Earth."

Thankful for the reprieve, Chakotay stood, grinning at her lightheartedly. "Thinking about hitching a ride?"

"I can commandeer it, you know," she reminded with a mock glare.

"I think my guest quarters are free."

He followed her to the corridor as the rest of them took their time saying their goodbyes. As they slipped into the turbo lift he watched the laughter shake her shoulders.

"_What_?"

"Nothing. It's just good to see Tom can still make you squirm." She folded her arms across her chest. "A spring cadet, Chakotay? Really?"

"Less Tom and more B'Elanna. She's been curious to the point of insubordination." He heaved a sigh. "I'm not sure what to tell her."

Though spoken as a statement, it was question that depended solely on Kathryn. She nodded, her eyes downcast, lips pressed to a tight line until finally she said, "I suppose that depends on who your new _girlfriend_ is."

A daring mirth crept out from her face, eyelashes making a slow sweep down to touch her cheeks. He reached to touch her, passing his thumb over her lips and making her gasp at the forwardness of the gesture. A promise built in his eyes; he stooped to lay a kiss on the crown of her head.

A long moment passed in comfortable silence until the lift opened to deck eleven and their starting point. Their end of journey was just beginning and he felt the excitement bubbling up inside him again. What designs _she_ had for the journey back to Earth, he couldn't say, but there was a bottle of Antarian cider on ice and a promise of unmitigated time alone…

With her.

Kathryn stopped short of the lab doors when they didn't open. She tossed a curious look over her shoulder and keyed the opening sequence.

Nothing.

He tapped his comm badge. "Chakotay to Dr. Zimmerman. We're ready to leave."

Still nothing.

"Janeway to Lieutenant Barclay."

Chakotay keyed the panel again then turned to Kathryn. "We're locked in."


End file.
